PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
29901-29950 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D16_PLUS | HG002complexvar | homalt | 98.1002 | 98.2699 | 97.9310 | 75.1286 | 284 | 5 | 284 | 6 | 5 | 83.3333 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l150_m0_e0 | * | 97.9275 | 97.9239 | 97.9310 | 91.1206 | 283 | 6 | 284 | 6 | 1 | 16.6667 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.5920 | 97.2554 | 97.9309 | 57.6692 | 17186 | 485 | 17181 | 363 | 345 | 95.0413 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.5920 | 97.2554 | 97.9309 | 57.6692 | 17186 | 485 | 17181 | 363 | 345 | 95.0413 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.6974 | 95.4955 | 97.9299 | 88.5024 | 636 | 30 | 615 | 13 | 5 | 38.4615 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.6974 | 95.4955 | 97.9299 | 88.5024 | 636 | 30 | 615 | 13 | 5 | 38.4615 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.8361 | 88.2463 | 97.9296 | 62.5291 | 473 | 63 | 473 | 10 | 9 | 90.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.7927 | 97.6562 | 97.9295 | 69.6398 | 1750 | 42 | 1750 | 37 | 33 | 89.1892 | |
| hfeng-pmm2 | INDEL | * | map_l125_m1_e0 | * | 98.2517 | 98.5762 | 97.9294 | 87.1694 | 2077 | 30 | 2081 | 44 | 7 | 15.9091 | |
| hfeng-pmm2 | SNP | ti | map_l250_m2_e1 | het | 98.4165 | 98.9088 | 97.9292 | 90.8817 | 3263 | 36 | 3263 | 69 | 7 | 10.1449 | |
| astatham-gatk | INDEL | D16_PLUS | HG002complexvar | het | 98.2855 | 98.6450 | 97.9287 | 68.7747 | 1092 | 15 | 851 | 18 | 11 | 61.1111 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.8028 | 97.6785 | 97.9275 | 46.3889 | 7279 | 173 | 7182 | 152 | 45 | 29.6053 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.9135 | 97.8996 | 97.9275 | 49.2246 | 3589 | 77 | 3591 | 76 | 67 | 88.1579 | |
| qzeng-custom | INDEL | * | HG002complexvar | * | 97.6731 | 97.4200 | 97.9274 | 54.9567 | 74953 | 1985 | 77253 | 1635 | 731 | 44.7095 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | het | 97.7232 | 97.5199 | 97.9274 | 51.5698 | 20250 | 515 | 20317 | 430 | 365 | 84.8837 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.5234 | 99.1268 | 97.9273 | 65.2174 | 6130 | 54 | 6142 | 130 | 33 | 25.3846 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e0 | het | 97.8087 | 97.6911 | 97.9266 | 82.2279 | 1227 | 29 | 1228 | 26 | 9 | 34.6154 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 98.1515 | 98.3778 | 97.9263 | 86.5655 | 849 | 14 | 850 | 18 | 4 | 22.2222 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.5468 | 91.3928 | 97.9261 | 61.6841 | 9206 | 867 | 9255 | 196 | 98 | 50.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.4344 | 96.9479 | 97.9258 | 61.8911 | 3780 | 119 | 3777 | 80 | 36 | 45.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.3394 | 98.7572 | 97.9251 | 69.6626 | 45134 | 568 | 45544 | 965 | 45 | 4.6632 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.3394 | 98.7572 | 97.9251 | 69.6626 | 45134 | 568 | 45544 | 965 | 45 | 4.6632 | |
| ghariani-varprowl | INDEL | I1_5 | map_l100_m2_e1 | homalt | 97.0093 | 96.1111 | 97.9245 | 77.2337 | 519 | 21 | 519 | 11 | 6 | 54.5455 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.9203 | 97.9167 | 97.9239 | 65.8796 | 564 | 12 | 566 | 12 | 9 | 75.0000 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e0 | * | 98.2547 | 98.5883 | 97.9233 | 87.9829 | 2165 | 31 | 2169 | 46 | 7 | 15.2174 | |
| ckim-vqsr | INDEL | D6_15 | * | homalt | 98.8887 | 99.8735 | 97.9231 | 55.6564 | 6318 | 8 | 6318 | 134 | 131 | 97.7612 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.0494 | 98.1771 | 97.9221 | 86.1908 | 377 | 7 | 377 | 8 | 2 | 25.0000 | |
| bgallagher-sentieon | SNP | tv | map_l150_m2_e0 | het | 98.6238 | 99.3381 | 97.9198 | 79.8967 | 7204 | 48 | 7202 | 153 | 20 | 13.0719 | |
| dgrover-gatk | SNP | * | map_l250_m2_e1 | het | 98.1329 | 98.3473 | 97.9194 | 91.5436 | 5177 | 87 | 5177 | 110 | 25 | 22.7273 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.5852 | 99.2612 | 97.9184 | 64.7490 | 55220 | 411 | 55320 | 1176 | 260 | 22.1088 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.8445 | 97.7707 | 97.9183 | 79.2041 | 1228 | 28 | 1223 | 26 | 7 | 26.9231 | |
| ckim-vqsr | INDEL | D16_PLUS | * | * | 97.9266 | 97.9363 | 97.9170 | 71.5505 | 6644 | 140 | 6628 | 141 | 105 | 74.4681 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7827 | 99.6639 | 97.9169 | 51.5925 | 9489 | 32 | 9495 | 202 | 199 | 98.5149 | |
| eyeh-varpipe | SNP | * | map_l125_m1_e0 | * | 98.7938 | 99.6867 | 97.9168 | 73.3897 | 45185 | 142 | 43853 | 933 | 38 | 4.0729 | |
| eyeh-varpipe | SNP | * | map_l150_m0_e0 | hetalt | 98.9474 | 100.0000 | 97.9167 | 79.8319 | 3 | 0 | 47 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 86.1595 | 76.9231 | 97.9167 | 68.0000 | 40 | 12 | 47 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | map_l150_m1_e0 | het | 96.3702 | 94.8718 | 97.9167 | 89.0411 | 37 | 2 | 47 | 1 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 97.0273 | 96.1538 | 97.9167 | 85.1852 | 50 | 2 | 47 | 1 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | segdup | * | 98.9474 | 100.0000 | 97.9167 | 95.5923 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | segdup | * | 98.9474 | 100.0000 | 97.9167 | 95.0515 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| jli-custom | INDEL | I16_PLUS | segdup | * | 98.9474 | 100.0000 | 97.9167 | 93.7419 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | segdup | * | 98.9474 | 100.0000 | 97.9167 | 95.8152 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| astatham-gatk | INDEL | * | map_l125_m0_e0 | homalt | 98.6014 | 99.2958 | 97.9167 | 88.3589 | 282 | 2 | 282 | 6 | 4 | 66.6667 | |
| bgallagher-sentieon | INDEL | * | map_l125_m0_e0 | homalt | 98.6014 | 99.2958 | 97.9167 | 88.2112 | 282 | 2 | 282 | 6 | 4 | 66.6667 | |
| astatham-gatk | INDEL | I16_PLUS | segdup | * | 98.9474 | 100.0000 | 97.9167 | 95.9459 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 97.7470 | 97.5779 | 97.9167 | 76.2963 | 282 | 7 | 282 | 6 | 5 | 83.3333 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6403 | 99.3747 | 97.9167 | 72.3397 | 5562 | 35 | 5546 | 118 | 106 | 89.8305 | |
| dgrover-gatk | INDEL | D6_15 | map_l150_m2_e1 | het | 98.9474 | 100.0000 | 97.9167 | 94.2238 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | segdup | * | 98.9474 | 100.0000 | 97.9167 | 95.9253 | 47 | 0 | 47 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l150_m2_e1 | het | 98.9474 | 100.0000 | 97.9167 | 92.6267 | 47 | 0 | 47 | 1 | 1 | 100.0000 | |